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PDBsum entry 1kw3

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protein ligands metals links
Oxidoreductase PDB id
1kw3
Jmol
Contents
Protein chain
288 a.a. *
Ligands
MPD ×2
Metals
FE2
Waters ×300
* Residue conservation analysis
PDB id:
1kw3
Name: Oxidoreductase
Title: Crystal structure of 2,3-dihydroxybiphenyal dioxygenase (bph a resolution
Structure: 2,3-dihydroxybiphenyl dioxygenase. Chain: b. Synonym: bphc, biphenyl-2,3-diol 1,2-dioxygenase. Engineered: yes
Source: Pseudomonas sp.. Organism_taxid: 307. Strain: kks102. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Octamer (from PDB file)
Resolution:
1.45Å     R-factor:   0.162     R-free:   0.177
Authors: N.Sato,Y.Uragami,T.Nishizaki,Y.Takahashi,G.Sazaki,K.Sugimoto T.Nonaka,E.Masai,M.Fukuda,T.Senda
Key ref:
N.Sato et al. (2002). Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase. J Mol Biol, 321, 621-636. PubMed id: 12206778 DOI: 10.1016/S0022-2836(02)00673-3
Date:
28-Jan-02     Release date:   28-Jan-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P17297  (BPHC_PSES1) -  Biphenyl-2,3-diol 1,2-dioxygenase
Seq:
Struc:
293 a.a.
288 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.13.11.39  - Biphenyl-2,3-diol 1,2-dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Biphenyl-2,3-diol + O2 = 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
Biphenyl-2,3-diol
Bound ligand (Het Group name = MPD)
matches with 46.67% similarity
+ O(2)
= 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
      Cofactor: Mn(2+) or Fe cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0022-2836(02)00673-3 J Mol Biol 321:621-636 (2002)
PubMed id: 12206778  
 
 
Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase.
N.Sato, Y.Uragami, T.Nishizaki, Y.Takahashi, G.Sazaki, K.Sugimoto, T.Nonaka, E.Masai, M.Fukuda, T.Senda.
 
  ABSTRACT  
 
BphC derived from Pseudomonas sp. strain KKS102 is an extradiol-cleaving catecholic dioxygenase. This enzyme contains a non-heme iron atom and plays an important role in degrading biphenyl/polychlorinated biphenyls (PCBs) in the microbe. To elucidate detailed structures of BphC reaction intermediates, crystal structures of the substrate-free form, the BphC-substrate complex, and the BphC-substrate-NO (nitric oxide) complex were determined. These crystal structures revealed (1) the binding site of the O(2) molecule in the coordination sphere and (2) conformational changes of His194 during the catalytic reaction. On the basis of these findings, we propose a catalytic mechanism for the extradiol-cleaving catecholic dioxygenase in which His194 seems to play three distinct roles. At the early stage of the catalytic reaction, His194 appears to act as a catalytic base, which likely deprotonates the hydroxyl group of the substrate. At the next stage, the protonated His194 seems to stabilize a negative charge on the O2 molecule located in the hydrophobic O2-binding cavity. Finally, protonated His194 seems to function as a proton donor, whose existence has been proposed.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereo view of the active-site structure of (a) the substrate-free form, (b) the ES(100) complex, and (c) the ES-NO complex. Hydrogen bonds are shown as red dotted lines. The NO molecule is shown in green. These Figures were prepared using the programs MOLSCRIPT[33] and Raster3D. [34]
Figure 8.
Figure 8. Proposed mechanism for extradiol ring cleavage of 2,3-DHBP by BphC. The ES-NO complex is presented in the center.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 321, 621-636) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21153851 A.J.Fielding, E.G.Kovaleva, E.R.Farquhar, J.D.Lipscomb, and L.Que (2011).
A hyperactive cobalt-substituted extradiol-cleaving catechol dioxygenase.
  J Biol Inorg Chem, 16, 341-355.
PDB codes: 3ojj 3ojk 3ojn 3ojt
18277980 E.G.Kovaleva, and J.D.Lipscomb (2008).
Versatility of biological non-heme Fe(II) centers in oxygen activation reactions.
  Nat Chem Biol, 4, 186-193.  
18826259 E.G.Kovaleva, and J.D.Lipscomb (2008).
Intermediate in the O-O bond cleavage reaction of an extradiol dioxygenase.
  Biochemistry, 47, 11168-11170.
PDB codes: 3ecj 3eck
19007887 J.D.Lipscomb (2008).
Mechanism of extradiol aromatic ring-cleaving dioxygenases.
  Curr Opin Struct Biol, 18, 644-649.  
18492808 J.P.Emerson, E.G.Kovaleva, E.R.Farquhar, J.D.Lipscomb, and L.Que (2008).
Swapping metals in Fe- and Mn-dependent dioxygenases: evidence for oxygen activation without a change in metal redox state.
  Proc Natl Acad Sci U S A, 105, 7347-7352.
PDB code: 3bza
18558332 K.Furukawa, and H.Fujihara (2008).
Microbial degradation of polychlorinated biphenyls: biochemical and molecular features.
  J Biosci Bioeng, 105, 433-449.  
18502868 M.J.Moonen, N.M.Kamerbeek, A.H.Westphal, S.A.Boeren, D.B.Janssen, M.W.Fraaije, and W.J.van Berkel (2008).
Elucidation of the 4-hydroxyacetophenone catabolic pathway in Pseudomonas fluorescens ACB.
  J Bacteriol, 190, 5190-5198.  
18502867 M.J.Moonen, S.A.Synowsky, W.A.van den Berg, A.H.Westphal, A.J.Heck, R.H.van den Heuvel, M.W.Fraaije, and W.J.van Berkel (2008).
Hydroquinone dioxygenase from pseudomonas fluorescens ACB: a novel member of the family of nonheme-iron(II)-dependent dioxygenases.
  J Bacteriol, 190, 5199-5209.  
18563190 T.P.Sipilä, A.K.Keskinen, M.L.Akerman, C.Fortelius, K.Haahtela, and K.Yrjälä (2008).
High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil.
  ISME J, 2, 968-981.  
18458966 V.Georgiev, T.Borowski, M.R.Blomberg, and P.E.Siegbahn (2008).
A comparison of the reaction mechanisms of iron- and manganese-containing 2,3-HPCD: an important spin transition for manganese.
  J Biol Inorg Chem, 13, 929-940.  
18019494 C.A.Joseph, and M.J.Maroney (2007).
Cysteine dioxygenase: structure and mechanism.
  Chem Commun (Camb), (), 3338-3349.  
17446402 E.G.Kovaleva, and J.D.Lipscomb (2007).
Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates.
  Science, 316, 453-457.
PDB codes: 2ig9 2iga
  16511281 K.Sugimoto, K.Matsufuzi, H.Ohnuma, M.Senda, M.Fukuda, and T.Senda (2006).
Crystallization and preliminary crystallographic analysis of the catechol 2,3-dioxygenase PheB from Bacillus stearothermophilus BR219.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 125-127.  
16734718 L.Siani, A.Viggiani, E.Notomista, A.Pezzella, and A.Di Donato (2006).
The role of residue Thr249 in modulating the catalytic efficiency and substrate specificity of catechol-2,3-dioxygenase from Pseudomonas stutzeri OX1.
  FEBS J, 273, 2963-2976.  
16791641 V.Georgiev, T.Borowski, and P.E.Siegbahn (2006).
Theoretical study of the catalytic reaction mechanism of MndD.
  J Biol Inorg Chem, 11, 571-585.  
16522801 X.Li, M.Guo, J.Fan, W.Tang, D.Wang, H.Ge, H.Rong, M.Teng, L.Niu, Q.Liu, and Q.Hao (2006).
Crystal structure of 3-hydroxyanthranilic acid 3,4-dioxygenase from Saccharomyces cerevisiae: a special subgroup of the type III extradiol dioxygenases.
  Protein Sci, 15, 761-773.  
15942729 A.Karlsson, J.V.Parales, R.E.Parales, D.T.Gibson, H.Eklund, and S.Ramaswamy (2005).
NO binding to naphthalene dioxygenase.
  J Biol Inorg Chem, 10, 483-489.
PDB codes: 1uuv 1uuw
16217642 J.P.Emerson, M.L.Wagner, M.F.Reynolds, L.Que, M.J.Sadowsky, and L.P.Wackett (2005).
The role of histidine 200 in MndD, the Mn(II)-dependent 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Arthrobacter globiformis CM-2, a site-directed mutagenesis study.
  J Biol Inorg Chem, 10, 751-760.  
15739104 K.D.Koehntop, J.P.Emerson, and L.Que (2005).
The 2-His-1-carboxylate facial triad: a versatile platform for dioxygen activation by mononuclear non-heme iron(II) enzymes.
  J Biol Inorg Chem, 10, 87-93.  
15735330 S.Saijo, Y.Yamada, T.Sato, N.Tanaka, T.Matsui, G.Sazaki, K.Nakajima, and Y.Matsuura (2005).
Structural consequences of hen egg-white lysozyme orthorhombic crystal growth in a high magnetic field: validation of X-ray diffraction intensity, conformational energy searching and quantitative analysis of B factors and mosaicity.
  Acta Crystallogr D Biol Crystallogr, 61, 207-217.
PDB codes: 1wtm 1wtn
15347689 A.Viggiani, L.Siani, E.Notomista, L.Birolo, P.Pucci, and A.Di Donato (2004).
The role of the conserved residues His-246, His-199, and Tyr-255 in the catalysis of catechol 2,3-dioxygenase from Pseudomonas stutzeri OX1.
  J Biol Chem, 279, 48630-48639.  
15028678 M.W.Vetting, L.P.Wackett, L.Que, J.D.Lipscomb, and D.H.Ohlendorf (2004).
Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases.
  J Bacteriol, 186, 1945-1958.
PDB codes: 1f1r 1f1u 1f1v 1f1x 1q0c 1q0o
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.